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I think the Hardest pokemon was Steven's Metagross...... U will need to use fire/fighting/ground moves to knock it, because it has high hp and defense...
Brawly's Makuhita (don't use Pokemon have higher level and not let your pokemon learn the TMs or HMs you not yet have actually in game ) :P It's hold Sitrus Berry and Brawly always use Full Restore on it :P
Not in game: Latios/Latias with Soul Dew :p
Slaking was hardest. It was the only pokemon that could stand up to my Blazikens legendary cut! Another cut and it was dead though. (Don't ask, it was on lvl 60. I evolved before fighting May for the first time, I love training)